calculate MSI STATUS using predefined MSI loci

Question

[J.F.Jiang]

Hi all,

I've designed 27 MSI probes to capture the reads.

As suggested, I used msisensor to obtain whether the loci was stable or not.

I restricted the msi site to those 27 MSI sites I designed, and used the default parameter for msi detection.

/bioinfo/software/msisensor2/msisensor2 msi -M /bioinfo/software/msisensor2/models_hg19/ -d ctdnawise-data/27_marker_microsatellites.list -t intermediate_bam/IDCL1017-GW9T0064D08_L3.markdup.bam -o example2.tumor.output

The output showed that only 7 have enough coverage

Since the reads distribution of these 27 sites seem quite normal, it made me quite confused.

Can anyone give me some suggestions to deal with such case?

Thanks, Junfeng